Dear all,

I have a problem in processing my microarrays data.And I know how the batch effect is structured,soI would like to remove batch effect using ComBat. But I also want to adjust for unknown sources of noise using sva. Is there a way of combining these two methods? And is it feasible that i run ComBat first, get the ComBat-adjusted matrix, and run sva on this? Is it bad practice to run a second adjustment on data which has already been adjusted by a different package. Thanks in advance.

Hello, i am checking SVA for estimating batches in my expression atlas. this expression atlas is composed my multiple experiments (different dates) and multiple tissues analysed. Contrarily to the general aim of this analysis, i am not interested in performing a DE analysis, but i am interested in normalizing this data for a following a network analysis. For this reason i'll consider the two methods:

(1) SVA : identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments. (2) ComBat: directly removing known batch effects using ComBat in SVA.

For the 1st method what will be the full model matrix that i have to set?

Hope it is clear, Thanks in advance.

Hi, I cannot download the bladderdata example and I am having problems with the format of the matrices to run ComBat.

How dat, batch and mod should be formatted?

Thanks.